ConnectionMatrix.java

/* $RCSfile$ * $Author: egonw $ * $Date: 2007-02-21 12:49:33 +0100 (Wed, 21 Feb 2007) $ * $Revision: 7986 $ * * Copyright (C) 2004-2007 The Chemistry Development Kit (CDK) project * * Contact: cdk-devel@lists.sourceforge.net * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU Lesser General Public License * as published by the Free Software Foundation; either version 2.1 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. */package org.openscience.cdk.graph.matrix;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IElectronContainer;
/** * Calculator for a connection matrix representation of this AtomContainer. An * adjacency matrix is a matrix of quare NxN matrix, where N is the number of * atoms in the AtomContainer. If the i-th and the j-th atom in the * atomcontainer share a bond, the element i,j in the matrix is set to the * bond order value. Otherwise it is zero. See {@cdk.cite TRI92}. * * @cdk.module standard * @cdk.keyword connection matrix * @cdk.dictref blue-obelisk:calculateConnectivityMatrix * * @author steinbeck * @cdk.created 2004-07-04 */00044publicclass ConnectionMatriximplementsIGraphMatrix {
/** * Returns the connection matrix representation of this AtomContainer. * * @param container The AtomContainer for which the matrix is calculated * @return A connection matrix representating this AtomContainer */00052publicstaticdouble[][] getMatrix(IAtomContainer container) {
IBond bond = null;
int indexAtom1;
int indexAtom2;
double[][] conMat = newdouble[container.getAtomCount()][container.getAtomCount()];
for (int f = 0; f < container.getElectronContainerCount(); f++)
{
bond = container.getBond(f);
indexAtom1 = container.getAtomNumber(bond.getAtom(0));
indexAtom2 = container.getAtomNumber(bond.getAtom(1));
conMat[indexAtom1][indexAtom2] = bond.getOrder();
conMat[indexAtom2][indexAtom1] = bond.getOrder();
}
return conMat;
}
}